I have a script that writes out the relative paths (i.e. ./path/to/file) of its varying outputs to a file.
in the output block of my WDL, I populate an Array[File] with these path via read_lines()
output {
Array[File] file_paths = read_lines("file_of_file_paths")
}
Running cromwell locally, this works just fine, and file_paths is populated with the delocalized paths of these files (confirmed by running a multi-task workflow to completion in which this is an intermediate task, and another task takes file_paths as an input). In FireCloud, however, file_paths is simply a list of each line of file_of_file_paths rather than a list of delocalized paths.